3UAN

Crystal structure of 3-O-sulfotransferase (3-OST-1) with bound PAP and heptasaccharide substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.844 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Dissecting the substrate recognition of 3-O-sulfotransferase for the biosynthesis of anticoagulant heparin.

Moon, A.F.Xu, Y.Woody, S.M.Krahn, J.M.Linhardt, R.J.Liu, J.Pedersen, L.C.

(2012) Proc.Natl.Acad.Sci.USA 109: 5265-5270

  • DOI: 10.1073/pnas.1117923109

  • PubMed Abstract: 
  • Heparin is a polysaccharide-based natural product that is used clinically as an anticoagulant drug. Heparan sulfate 3-O-sulfotransferase (3-OST) is an enzyme that transfers a sulfo group to the 3-OH position of a glucosamine unit. 3-OST is present in ...

    Heparin is a polysaccharide-based natural product that is used clinically as an anticoagulant drug. Heparan sulfate 3-O-sulfotransferase (3-OST) is an enzyme that transfers a sulfo group to the 3-OH position of a glucosamine unit. 3-OST is present in multiple isoforms, and the polysaccharides modified by these different isoforms perform distinct biological functions. 3-OST isoform 1 (3-OST-1) is the key enzyme for the biosynthesis of anticoagulant heparin. Here, we report the crystal structure of the ternary complex of 3-OST-1, 3'-phosphoadenosine 5'-phosphate, and a heptasaccharide substrate. Comparisons to previously determined structures of 3-OST-3 reveal unique binding modes used by the different isoforms of 3-OST for distinguishing the fine structures of saccharide substrates. Our data demonstrate that the saccharide substrates display distinct conformations when interacting with the different 3-OST isoforms. Site-directed mutagenesis data suggest that several key amino residues, including Lys259, Thr256, and Trp283 in 3-OST-3 and Arg268 in 3-OST-1, play important roles in substrate binding and specificity between isoforms. These results deepen our understanding of the biosynthetic mechanism of heparan sulfate and provide structural information for engineering enzymes for an enhanced biosynthetic approach to heparin production.


    Organizational Affiliation

    Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heparan sulfate glucosamine 3-O-sulfotransferase 1
A, B
269Mus musculusMutation(s): 0 
Gene Names: Hs3st1 (3ost, 3ost1)
EC: 2.8.2.23
Find proteins for O35310 (Mus musculus)
Go to UniProtKB:  O35310
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A3P
Query on A3P

Download SDF File 
Download CCD File 
A, B
ADENOSINE-3'-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
WHTCPDAXWFLDIH-KQYNXXCUSA-N
 Ligand Interaction
NGY
Query on NGY

Download SDF File 
Download CCD File 
A, B
2-(acetylamino)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose
Sulfated glycosaminoglycan
C8 H15 N O9 S
WJFVEEAIYIOATH-PVFLNQBWSA-N
 Ligand Interaction
SGN
Query on SGN

Download SDF File 
Download CCD File 
A, B
N,O6-DISULFO-GLUCOSAMINE
C6 H13 N O11 S2
DQTRACMFIGDHSN-UKFBFLRUSA-N
 Ligand Interaction
BDP
Query on BDP

Download SDF File 
Download CCD File 
A, B
BETA-D-GLUCOPYRANURONIC ACID
D-GLUCURONIC ACID
C6 H10 O7
AEMOLEFTQBMNLQ-QIUUJYRFSA-N
 Ligand Interaction
IDS
Query on IDS

Download SDF File 
Download CCD File 
A, B
2-O-sulfo-alpha-L-idopyranuronic acid
O2-SULFO-GLUCURONIC ACID
C6 H10 O10 S
COJBCAMFZDFGFK-VCSGLWQLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.844 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.883α = 90.00
b = 62.168β = 95.16
c = 86.373γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
StructureStudiodata collection
MOLREPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-04
    Type: Initial release
  • Version 1.1: 2012-04-18
    Type: Database references
  • Version 1.2: 2012-04-25
    Type: Database references